Basepair was founded in direct response to the challenges I was personally facing with Next Generation Sequencing (NGS) analysis while working at Harvard Medical School and other research institutions. NGS has witnessed a data deluge three times larger than Moore’s Law (i.e., the number of transistors in a dense integrated circuit doubles approximately every two years). Even simple operations like zipping, copying, and parsing files can take several minutes. As a result, computing resources are constantly stressed; in fact,  I was warned — more than once — by system admins to submit fewer jobs and delete files…or else. Not exactly what a research scientist wants to hear when he has many, many GBs of analysis to run.  In addition to the resource constraints and, given the complexity of running things on a cluster, scientists are also dependent on bioinformaticians for running standard pipelines.  

With Basepair, I wanted to build the type of software application that I wished I had as a research scientist.  The company’s goals have always been to develop an application that requires less than a minute of training to use, minimizes hands-on time, has ready-to-use pipelines for major NGS applications, and produces easy-to-interpret results:  That is exactly what my team and I have done.

Basepair’s growth has been truly organic — driven completely by our users. The company started with three NGS pipelines — and now we have 20 (and counting)!  You can now use Basepair for variant calling (DNA-Seq), differential expression (RNA-Seq), peak calling (ChIP-Seq), open chromatin (ATAC-Seq), and more. We even developed a pipeline for automatically submitting data to GEO for meeting publishing requirements.

In numbers



Parallel analysis

We constantly update existing workflows, too. For example, the differential expression pipeline now generates heatmaps and volcano plots.  And the peak-calling pipeline creates a figure showing genomic distribution of peaks.

One of the key objectives behind starting Basepair was to create software that evolves with users’ needs. In addition to the feedback we get directly, we have a lot of analytics under the hood to understand how our software is used. One of our favorites: on average it takes less than a minute to add and analyze a sample on Basepair.  That’s not a typo!

We’ve also made several technical improvements: automatic start of analysis after uploads are completed, multi-file uploads (when your sequencing core breaks the data into several files), and more.

We thank those of you who jumped right in and became early adopters, and we hope we’ve significantly accelerated your NGS analysis and made your life easier.  And to everyone else reading this post…why not give it a try for free and see for yourself?